Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014842.1 Kokia drynarioides strain JFW-HI SEQ_129885, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 130246
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 240 characters in sequence are not A, C, G, or T
Found at i:612 original size:29 final size:29
Alignment explanation
Indices: 507--652 Score: 102
Period size: 29 Copynumber: 4.9 Consensus size: 29
497 CCCTAAAGGT
*
507 CCCT-AAACTGTCCAAAAATTCCATTTTTGA
1 CCCTAAAACT-TCCAAAAATTCCA-TTTTAA
* ** *
537 -CCTCGAAACTTCCAAAAATTATATTTTTA
1 CCCT-AAAACTTCCAAAAATTCCATTTTAA
** * *
566 CCC-ACGTACTCCCTAAAATTCCATTTTAA
1 CCCTA-AAACTTCCAAAAATTCCATTTTAA
*
595 CCCTAAAACTTCCAAAAATTCTATTTTTAA
1 CCCTAAAACTTCCAAAAATTCCA-TTTTAA
*
625 TCCC-AAAACTTCTAAAAATTACCATTTT
1 -CCCTAAAACTTCCAAAAATT-CCATTTT
653 GCCCTTATAT
Statistics
Matches: 90, Mismatches: 18, Indels: 16
0.73 0.15 0.13
Matches are distributed among these distances:
29 41 0.46
30 39 0.43
31 10 0.11
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
CCCTAAAACTTCCAAAAATTCCATTTTAA
Found at i:640 original size:58 final size:60
Alignment explanation
Indices: 542--685 Score: 147
Period size: 59 Copynumber: 2.5 Consensus size: 60
532 TTTGACCTCG
* **
542 AAACTTCCAAAAATTATATTTTT-ACCCACGTACTCCCT-AAAATT-CCATTTTAACCCTA
1 AAACTTCCAAAAATTCTATTTTTAACCCACAAACTCCCTAAAAATTACCATTTT-ACCCTA
* * *
600 AAACTTCCAAAAATTCTATTTTTAATCCCA-AAACT-TCTAAAAATTACCATTTTGCCCTT
1 AAACTTCCAAAAATTCTATTTTTAA-CCCACAAACTCCCTAAAAATTACCATTTTACCCTA
* *
659 ATA-TGTCCAATAATTCTATTTTTAACC
1 AAACT-TCCAAAAATTCTATTTTTAACC
686 TCGAAACTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
58 27 0.37
59 35 0.48
60 11 0.15
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (60 bp):
AAACTTCCAAAAATTCTATTTTTAACCCACAAACTCCCTAAAAATTACCATTTTACCCTA
Found at i:644 original size:59 final size:59
Alignment explanation
Indices: 506--683 Score: 143
Period size: 59 Copynumber: 3.0 Consensus size: 59
496 GCCCTAAAGG
* * * * *
506 TCCCTAAACTGTCCAAAAATTCCATTTTTGA-CCTCGAAACTTCCAAAAATTATATTTTT-A
1 TCCCAAAACTCTCTAAAAATTCCA-TTTT-ACCCT-AAAACTTCCAAAAATTCTATTTTTAA
** *
566 -CCCACGTACTCCCT-AAAATTCCATTTTAACCCTAAAACTTCCAAAAATTCTATTTTTAA
1 TCCCA-AAACTCTCTAAAAATTCCATTTT-ACCCTAAAACTTCCAAAAATTCTATTTTTAA
* * * *
625 TCCCAAAACT-TCTAAAAATTACCATTTTGCCCTTATA-TGTCCAATAATTCTATTTTTAA
1 TCCCAAAACTCTCTAAAAATT-CCATTTTACCCTAAAACT-TCCAAAAATTCTATTTTTAA
684 CCTCGAAACT
Statistics
Matches: 95, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
58 30 0.32
59 50 0.53
60 15 0.16
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (59 bp):
TCCCAAAACTCTCTAAAAATTCCATTTTACCCTAAAACTTCCAAAAATTCTATTTTTAA
Found at i:759 original size:118 final size:118
Alignment explanation
Indices: 637--858 Score: 275
Period size: 118 Copynumber: 1.9 Consensus size: 118
627 CCAAAACTTC
* * * *
637 TAAAAATTACCATTTT-GCCCTTATATGTCCAATAATTCTATTTTTAACCTCGAAACTTTTGAAA
1 TAAAAATTACCATTTTACCCCTGA-ATGTCCAAAAATTCCATTTTTAACCTCGAAACTTTTGAAA
701 ATTACCCTTTTACCCCCGAATGTCTAAAAATTCCATTTTTGATCTTGATTTTCT
65 ATTACCCTTTTACCCCCGAATGTCTAAAAATTCCATTTTTGATCTTGATTTTCT
* * * *** * *
755 TAAAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCGTTTTTTATCTCGATTTTTTTTAAAG
1 TAAAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTAACCTCGAAACTTTTGAAAA
* * * **
820 TTACCGTTTTACTCTCGGGTGTCTAAAAATTCCATTTTT
66 TTACCCTTTTACCCCCGAATGTCTAAAAATTCCATTTTT
859 AACCCCGACC
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
118 81 0.94
119 5 0.06
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.43
Consensus pattern (118 bp):
TAAAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTAACCTCGAAACTTTTGAAAA
TTACCCTTTTACCCCCGAATGTCTAAAAATTCCATTTTTGATCTTGATTTTCT
Found at i:793 original size:59 final size:58
Alignment explanation
Indices: 580--888 Score: 194
Period size: 59 Copynumber: 5.2 Consensus size: 58
570 CGTACTCCCT
* * * * * ** *
580 AAAATT-CCATTTTAACCCTAAAACT-TCCAAAAATTCTATTTTTAATCCCAAAACTTCTA
1 AAAATTACCATTTTACCCCT-GAA-TGTCCAAAAATTCCATTTTTAATCTC-GATTTTTTA
* * * * * ** *
639 AAAATTACCATTTT-GCCCTTATATGTCCAATAATTCTATTTTTAACCTCGAAACTTTTG
1 AAAATTACCATTTTACCCCTGA-ATGTCCAAAAATTCCATTTTTAATCTCG-ATTTTTTA
* * * * *
698 AAAATTACCCTTTTACCCCCGAATGTCTAAAAATTCCATTTTTGATCTTGATTTTCTTA
1 AAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTAATCTCGATTTT-TTA
* * *
757 AAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCGTTTTTTATCTCGATTTTTTTT
1 AAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTAATCTCGA-TTTTTTA
* * * ** * * * ** *
816 AAAGTTACCGTTTTA-CTCTCGGGTGTCTAAAAATTCCATTTTTAACCCCGACCTTTCA
1 AAAATTACCATTTTACCCCT-GAATGTCCAAAAATTCCATTTTTAATCTCGATTTTTTA
874 CAAAATTACCATTTT
1 -AAAATTACCATTTT
889 GCCCTCGAGA
Statistics
Matches: 197, Mismatches: 44, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
58 11 0.06
59 171 0.87
60 15 0.08
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.40
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTAATCTCGATTTTTTA
Found at i:4869 original size:21 final size:21
Alignment explanation
Indices: 4823--4869 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
4813 CTTATGATAG
*
4823 TTCTATCGATACAAGTGAGAC
1 TTCTATCGATACAAGTCAGAC
* *
4844 ATCTATTGATACAAGTCATG-C
1 TTCTATCGATACAAGTCA-GAC
4865 TTCTA
1 TTCTA
4870 CCAATACTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (21 bp):
TTCTATCGATACAAGTCAGAC
Found at i:9292 original size:23 final size:23
Alignment explanation
Indices: 9266--9310 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
9256 TCTCACACTT
*
9266 TTTCTTACTC-TTTTCTTTTTGTA
1 TTTC-TACTCATTTTCATTTTGTA
9289 TTTCTACTCATTTTCATTTTGT
1 TTTCTACTCATTTTCATTTTGT
9311 TCTTTTCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.11, C:0.18, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTCTACTCATTTTCATTTTGTA
Found at i:12253 original size:9 final size:9
Alignment explanation
Indices: 12239--12297 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
12229 TTTGAAATAC
12239 AAAATTATT
1 AAAATTATT
12248 AAAATTATT
1 AAAATTATT
* *
12257 ATATTATTTTTT
1 A-A--AATTATT
*
12269 AAAAATA-T
1 AAAATTATT
12277 AAAATTATT
1 AAAATTATT
12286 AAAATTATT
1 AAAATTATT
12295 AAA
1 AAA
12298 TAATTTTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 7 0.17
9 25 0.62
10 1 0.03
11 1 0.03
12 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AAAATTATT
Found at i:12268 original size:38 final size:38
Alignment explanation
Indices: 12208--12304 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 38
12198 GCAAATTACT
* *
12208 TTAAAATTTTTAAAATTATTTTTT-GAAATACAAAATTA
1 TTAAAATTATT-AAATTATTTTTTAAAAATACAAAATTA
* *
12246 TTAAAATTATTATATTATTTTTTAAAAATATAAAATTA
1 TTAAAATTATTAAATTATTTTTTAAAAATACAAAATTA
*
12284 TTAAAATTATTAAATAATTTT
1 TTAAAATTATTAAATTATTTT
12305 AATTTCTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 11 0.21
38 41 0.79
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (38 bp):
TTAAAATTATTAAATTATTTTTTAAAAATACAAAATTA
Found at i:15814 original size:24 final size:24
Alignment explanation
Indices: 15760--15835 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
15750 GAAAAGGAAG
*
15760 GTTTTTCTTTGTCAAAATAAAAAA
1 GTTTTTTTTTGTCAAAATAAAAAA
15784 GTTTTTTTTTGTCAAAATAAAAAA
1 GTTTTTTTTTGTCAAAATAAAAAA
* *
15808 GTTTTTTTTTTGTTAAATAGAAAAAA
1 G-TTTTTTTTTGTCAAA-ATAAAAAA
15834 GT
1 GT
15836 GTTCTTTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
24 24 0.51
25 15 0.32
26 8 0.17
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (24 bp):
GTTTTTTTTTGTCAAAATAAAAAA
Found at i:20384 original size:40 final size:40
Alignment explanation
Indices: 20340--20418 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
20330 AAAGATCACC
* *
20340 ATTTTTAACTTTTACAATAGAGCTTTTGACTAGAATTACA
1 ATTTTTAACTTTTACAAGAGAGCTTTTGACTAAAATTACA
*
20380 ATTTTTAGCTTTTACAAGAGAGCTTTTGACTAAAATTAC
1 ATTTTTAACTTTTACAAGAGAGCTTTTGACTAAAATTAC
20419 TTCTATATCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (40 bp):
ATTTTTAACTTTTACAAGAGAGCTTTTGACTAAAATTACA
Found at i:42771 original size:10 final size:10
Alignment explanation
Indices: 42756--42824 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 10
42746 GCTTTGCCTC
*
42756 GGTTTCTGCT
1 GGTTTCAGCT
*
42766 GGTTTCGGCT
1 GGTTTCAGCT
42776 CGGTTTCAGCT
1 -GGTTTCAGCT
*
42787 GGCTTC-GCCT
1 GGTTTCAG-CT
42797 CGGTTTCAGCT
1 -GGTTTCAGCT
* *
42808 GGCTTCACCT
1 GGTTTCAGCT
42818 CGGTTTC
1 -GGTTTC
42825 GGCCAGAGCT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
9 1 0.02
10 24 0.51
11 21 0.45
12 1 0.02
ACGTcount: A:0.04, C:0.29, G:0.29, T:0.38
Consensus pattern (10 bp):
GGTTTCAGCT
Found at i:42777 original size:21 final size:21
Alignment explanation
Indices: 42745--42824 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
42735 AGCTTCTGTG
* *
42745 GGCTTTGCCTCGGTTTCTGCT
1 GGCTTCGCCTCGGTTTCAGCT
* *
42766 GGTTTCGGCTCGGTTTCAGCT
1 GGCTTCGCCTCGGTTTCAGCT
42787 GGCTTCGCCTCGGTTTCAGCT
1 GGCTTCGCCTCGGTTTCAGCT
*
42808 GGCTTCACCTCGGTTTC
1 GGCTTCGCCTCGGTTTC
42825 GGCCAGAGCT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.04, C:0.30, G:0.29, T:0.38
Consensus pattern (21 bp):
GGCTTCGCCTCGGTTTCAGCT
Found at i:45556 original size:68 final size:66
Alignment explanation
Indices: 45483--45744 Score: 213
Period size: 68 Copynumber: 3.9 Consensus size: 66
45473 CTCAAGGTGC
* * *
45483 ATACTTATTAAAGTATTTTGCCTTCTCATGCACTTAGCTTTTCAAAGCTTTCAACCTTTTCGAG-
1 ATACTTCTTAAAGTACTTTACCTTCTCA-GCACTTAGCTTTTCAAAGCTTTCAACCTTTTCGAGC
*
45547 TT
65 GT
* ** * **
45549 AAGTACTTCTTAAAGTACATTATATTCTCAAGCACTTATCTTTTCAAATATTTCAACCTTCTT-G
1 -A-TACTTCTTAAAGTACTTTACCTTCTC-AGCACTTAGCTTTTCAAAGCTTTCAACCTT-TTCG
45613 AGCCGT
62 AG-CGT
* * * *
45619 ATACTTCTTAAAGTACTTTACCTTCTCGAGCATTTAGTTTTTCAAAGCTTTCATCCTTTTCGGGA
1 ATACTTCTTAAAGTACTTTACCTTCTC-AGCACTTAGCTTTTCAAAGCTTTCAACCTTTTCGAG-
* *
45684 TGC
64 CGT
** ** * ** *
45687 ATGTTTCTTAAAGTACTTCGCCTTCTTAAGGGCTTAGCTTTTCAAAACTTTCAACCTT
1 ATACTTCTTAAAGTACTTTACCTTC-TCAGCACTTAGCTTTTCAAAGCTTTCAACCTT
45745 CTTAGTTTCC
Statistics
Matches: 153, Mismatches: 35, Indels: 13
0.76 0.17 0.06
Matches are distributed among these distances:
67 3 0.02
68 144 0.94
69 5 0.03
70 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (66 bp):
ATACTTCTTAAAGTACTTTACCTTCTCAGCACTTAGCTTTTCAAAGCTTTCAACCTTTTCGAGCG
T
Found at i:45728 original size:136 final size:135
Alignment explanation
Indices: 45483--45747 Score: 304
Period size: 136 Copynumber: 1.9 Consensus size: 135
45473 CTCAAGGTGC
* *
45483 ATACTTATTAAAGTATTTTGCCTTCTCATGCACTTAGCTTTTCAAAGCTTTCAACCTTTTCGAGT
1 ATACTTATTAAAGTACTTTACCTTCTCATGCACTTAGCTTTTCAAAGCTTTCAACCTTTTCGAGT
* * *
45548 TAAGTACTTCTTAAAGTACATTATATTCTCAAGCACTTATCTTTTCAAATA-TTTCAACCTTCTT
66 CAAGTA-TTCTTAAAGTACATTACATTCTCAAGCACTTAGCTTTTCAAA-ACTTTCAACCTTCTT
45612 GAGCCGT
129 GAGCCGT
* * * * *
45619 ATACTTCTTAAAGTACTTTACCTTCTCGA-GCATTTAGTTTTTCAAAGCTTTCATCCTTTTCGGG
1 ATACTTATTAAAGTACTTTACCTTCTC-ATGCACTTAGCTTTTCAAAGCTTTCAACCTTTTCGAG
* * * * **
45683 ATGCATGT-TTCTTAAAGTAC-TTCGCCTTCTTAAGGGCTTAGCTTTTCAAAACTTTCAACCTTC
65 -T-CAAGTATTCTTAAAGTACATT-ACATTCTCAAGCACTTAGCTTTTCAAAACTTTCAACCTTC
45746 TT
127 TT
45748 AGTTTCCATA
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
135 3 0.03
136 100 0.93
137 2 0.02
138 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (135 bp):
ATACTTATTAAAGTACTTTACCTTCTCATGCACTTAGCTTTTCAAAGCTTTCAACCTTTTCGAGT
CAAGTATTCTTAAAGTACATTACATTCTCAAGCACTTAGCTTTTCAAAACTTTCAACCTTCTTGA
GCCGT
Found at i:47596 original size:18 final size:18
Alignment explanation
Indices: 47587--47691 Score: 75
Period size: 18 Copynumber: 5.6 Consensus size: 18
47577 TATAGTATAT
47587 GGTTTGCATACATATTAG
1 GGTTTGCATACATATTAG
* *
47605 GGTTTGCATAAATATAAG
1 GGTTTGCATACATATTAG
** * **
47623 GGTTCACTTACATACAAG
1 GGTTTGCATACATATTAG
*
47641 GGTTTGCATATATATATATAAG
1 GGTTTGC--ATACATAT-T-AG
** *
47663 GGTTCACATACATATAAG
1 GGTTTGCATACATATTAG
47681 GGTTTGCATAC
1 GGTTTGCATAC
47692 TCGGGCTCTT
Statistics
Matches: 64, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
18 45 0.70
20 12 0.19
22 7 0.11
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.34
Consensus pattern (18 bp):
GGTTTGCATACATATTAG
Found at i:47635 original size:36 final size:38
Alignment explanation
Indices: 47593--47690 Score: 137
Period size: 40 Copynumber: 2.6 Consensus size: 38
47583 ATATGGTTTG
*
47593 CATACATATTAGGGTTTGCATA-A-ATATAAGGGTTCA
1 CATACATATAAGGGTTTGCATATATATATAAGGGTTCA
* *
47629 CTTACATACAAGGGTTTGCATATATATATATAAGGGTTCA
1 CATACATATAAGGGTTTGC--ATATATATATAAGGGTTCA
47669 CATACATATAAGGGTTTGCATA
1 CATACATATAAGGGTTTGCATA
47691 CTCGGGCTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
36 16 0.30
38 6 0.11
39 1 0.02
40 30 0.57
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (38 bp):
CATACATATAAGGGTTTGCATATATATATAAGGGTTCA
Found at i:47852 original size:23 final size:23
Alignment explanation
Indices: 47822--47868 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
47812 ATTTAGGAAG
47822 AATGTCAAATATAGAATCGAATT
1 AATGTCAAATATAGAATCGAATT
47845 AATGTCAAATATAGAATCGAATT
1 AATGTCAAATATAGAATCGAATT
47868 A
1 A
47869 TAATCATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.30
Consensus pattern (23 bp):
AATGTCAAATATAGAATCGAATT
Found at i:49331 original size:19 final size:19
Alignment explanation
Indices: 49307--49345 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
49297 AAGTGGAAAG
*
49307 TAAGTTTACTTCTTAATTC
1 TAAGTTTACTTCCTAATTC
49326 TAAGTTTACTTCCTAATTC
1 TAAGTTTACTTCCTAATTC
49345 T
1 T
49346 GGTATAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (19 bp):
TAAGTTTACTTCCTAATTC
Found at i:51654 original size:9 final size:9
Alignment explanation
Indices: 51637--51780 Score: 53
Period size: 9 Copynumber: 15.3 Consensus size: 9
51627 ATATAAAATG
*
51637 AAAATTATA
1 AAAAATATA
51646 AAAAATATA
1 AAAAATATA
*
51655 AAAATTGA-A
1 AAAAAT-ATA
*
51664 AAAAATTATT
1 AAAAA-TATA
*
51674 AGAAAT-TA
1 AAAAATATA
51682 AGAGAGAAT-TA
1 A-A-A-AATATA
51693 TAAAAATAATA
1 -AAAAAT-ATA
*
51704 TAAAATTATA
1 -AAAAATATA
*
51714 AAAAAT-TT
1 AAAAATATA
* *
51722 AGAACTATA
1 AAAAATATA
* *
51731 AAAATTATT
1 AAAAATATA
*
51740 AAAAATATT
1 AAAAATATA
*
51749 AAAAATTTA
1 AAAAATATA
51758 AAGAGAATATA
1 AA-A-AATATA
*
51769 TAAAATATA
1 AAAAATATA
51778 AAA
1 AAA
51781 TATAAAAGAA
Statistics
Matches: 101, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
8 7 0.07
9 60 0.59
10 13 0.13
11 20 0.20
12 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.29
Consensus pattern (9 bp):
AAAAATATA
Found at i:51745 original size:36 final size:35
Alignment explanation
Indices: 51686--51787 Score: 93
Period size: 36 Copynumber: 2.9 Consensus size: 35
51676 AAATTAAGAG
*
51686 AGAATTATAAAAATAATATAAAATTATAAAAAATTT
1 AGAACTATAAAAATAATATAAAA-TATAAAAAATTT
* *
51722 AGAACTATAAAAATTAT-TAAAAATATTAAAAATTT
1 AGAACTATAAAAATAATAT-AAAATATAAAAAATTT
* *
51757 AAAGAGAATAT-ATAA-AATATAAAATATAAAA
1 --AGA-ACTATAAAAATAATATAAAATATAAAA
51788 GAAATGATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
35 12 0.22
36 31 0.57
37 7 0.13
38 4 0.07
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (35 bp):
AGAACTATAAAAATAATATAAAATATAAAAAATTT
Found at i:60384 original size:21 final size:21
Alignment explanation
Indices: 60360--60431 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
60350 AGAGTTTTTA
*
60360 GTATCAGTAGAAGTAAGACTT
1 GTATCGGTAGAAGTAAGACTT
*
60381 GTATTGGTAGAAG--AGTCACTT
1 GTATCGGTAGAAGTAAG--ACTT
* **
60402 GTATCGGTAGAACTATCACTT
1 GTATCGGTAGAAGTAAGACTT
60423 GTATCGGTA
1 GTATCGGTA
60432 AGAGTCTGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 2 0.05
21 39 0.95
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAAGTAAGACTT
Found at i:65841 original size:24 final size:23
Alignment explanation
Indices: 65788--65841 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
65778 AATTTATATT
**
65788 TTTTACATTAATATTTTAAATTTA
1 TTTTA-ATTAATATTTTAAATAAA
*
65812 TCTTAATTATATATTTTAAATAAA
1 TTTTAATTA-ATATTTTAAATAAA
65836 TTTTAA
1 TTTTAA
65842 AGAATTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTAATTAATATTTTAAATAAA
Found at i:68536 original size:109 final size:110
Alignment explanation
Indices: 68402--68621 Score: 322
Period size: 111 Copynumber: 2.0 Consensus size: 110
68392 AAATCAAATT
*
68402 GCCTAATTGCTAAAATGAATGGTAAAACTAAACTTAAAA-A-ATAAAAACTCACCAACTTCCTAA
1 GCCTAATTGCTAAAATGAATGGTAAAACTAAACTTAAAACACA-AAAAAATCACCAACTTCCTAA
*
68465 AACAAGCAGAGA-AAAAAGGGACAAATTTGATTGAATCATATATTCA
65 AACAAGCAGAGACAAAAAGGG-CAAATTTGATCGAATCATATATTCA
* *
68511 GCCTAATTGCTAAAATGGA-GAGTAAAACTAAACTTAAAACACCAAAAAAATCACTAACTTCCTA
1 GCCTAATTGCTAAAATGAATG-GTAAAACTAAACTTAAAACA-CAAAAAAATCACCAACTTCCTA
* *
68575 AAACAAGTAGAGACAAAATGGGCAAATTTGATCGAATCATATATTCA
64 AAACAAGCAGAGACAAAAAGGGCAAATTTGATCGAATCATATATTCA
68622 ATGTAACAGC
Statistics
Matches: 100, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
108 1 0.01
109 36 0.36
110 1 0.01
111 54 0.54
112 8 0.08
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (110 bp):
GCCTAATTGCTAAAATGAATGGTAAAACTAAACTTAAAACACAAAAAAATCACCAACTTCCTAAA
ACAAGCAGAGACAAAAAGGGCAAATTTGATCGAATCATATATTCA
Found at i:69875 original size:52 final size:52
Alignment explanation
Indices: 69804--69969 Score: 253
Period size: 52 Copynumber: 3.2 Consensus size: 52
69794 AAAAAGGTCT
*
69804 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTTC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTATACGGATTATAAGGTTC
* * *
69856 GATGACTATGTGTCATCGTGAGTATATGAATCCTATACGAATTATGAGTTTC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTATACGGATTATAAGGTTC
**
69908 GATGACTATGTGTCATCGTGAGTATATGAATTCCTATACGGAACA-AGAGGTTC
1 GATGACTATGTGTCATCGTGAGTATATGAA-TCCTATACGGATTATA-AGGTTC
69961 GATGACTAT
1 GATGACTAT
69970 ATATTATCGT
Statistics
Matches: 103, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
52 78 0.76
53 25 0.24
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTATACGGATTATAAGGTTC
Found at i:70971 original size:14 final size:15
Alignment explanation
Indices: 70946--70974 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
70936 ATAAAGTAAC
70946 GATAAGATGAACAGT
1 GATAAGATGAACAGT
70961 GATAA-ATGAACAGT
1 GATAAGATGAACAGT
70975 AAAACATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.07, G:0.24, T:0.21
Consensus pattern (15 bp):
GATAAGATGAACAGT
Found at i:71281 original size:109 final size:108
Alignment explanation
Indices: 71072--71269 Score: 276
Period size: 109 Copynumber: 1.9 Consensus size: 108
71062 CTTAAAAAAA
* * **
71072 AAAAAATCAAAACTTACCAACTTCCTAAAACAAGCAGAGAAAAAAGGGGCAAATTTTATCGAATC
1 AAAAAATCAAAACTCACCAACTTCCTAAAACAAGCAGAGAAAAAACGGGCAAATTCGATCGAATC
* ** *
71137 ATATATTCAGCCTAATTGCTAAAATGGAGAGTAAAACTAAACTT
66 ATATATTCAGCATAA-TGCTAAAATAAAGACTAAAACTAAACTT
* *
71181 AAAAAATCAAAACTCACCAACTTCCTAAAACAAGCAGAG-AAAATCGGGTAAATTCGATCGAATC
1 AAAAAATCAAAACTCACCAACTTCCTAAAACAAGCAGAGAAAAAACGGGCAAATTCGATCGAATC
71245 ATATATTCAGCATAA-GC-AAAATAAA
66 ATATATTCAGCATAATGCTAAAATAAA
71270 AATGTACTAA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
105 6 0.08
106 2 0.03
108 34 0.43
109 38 0.47
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.21
Consensus pattern (108 bp):
AAAAAATCAAAACTCACCAACTTCCTAAAACAAGCAGAGAAAAAACGGGCAAATTCGATCGAATC
ATATATTCAGCATAATGCTAAAATAAAGACTAAAACTAAACTT
Found at i:72328 original size:11 final size:11
Alignment explanation
Indices: 72312--72344 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
72302 CTCTCTAGCC
72312 TTTCCCTTCCA
1 TTTCCCTTCCA
72323 TTTCCCTTCCA
1 TTTCCCTTCCA
72334 TTTCCCTTCCA
1 TTTCCCTTCCA
72345 CTCCTTTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (11 bp):
TTTCCCTTCCA
Found at i:77370 original size:69 final size:69
Alignment explanation
Indices: 77290--77430 Score: 282
Period size: 69 Copynumber: 2.0 Consensus size: 69
77280 ATTTTATTTT
77290 AATAGAAACCAATAAAAATATGTATACAATGAGATTTGAACCCATGTTAATTATATTAATAAAAC
1 AATAGAAACCAATAAAAATATGTATACAATGAGATTTGAACCCATGTTAATTATATTAATAAAAC
77355 CTTA
66 CTTA
77359 AATAGAAACCAATAAAAATATGTATACAATGAGATTTGAACCCATGTTAATTATATTAATAAAAC
1 AATAGAAACCAATAAAAATATGTATACAATGAGATTTGAACCCATGTTAATTATATTAATAAAAC
77424 CTTA
66 CTTA
77428 AAT
1 AAT
77431 TTTTCACTCA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (69 bp):
AATAGAAACCAATAAAAATATGTATACAATGAGATTTGAACCCATGTTAATTATATTAATAAAAC
CTTA
Found at i:77994 original size:13 final size:12
Alignment explanation
Indices: 77978--78023 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
77968 TGATTCGATT
*
77978 TTTTTATATTAA
1 TTTTTATATTTA
*
77990 GTTTTTATTTTTA
1 -TTTTTATATTTA
78003 TTTTTTATATTTA
1 -TTTTTATATTTA
78016 TTTTTATA
1 TTTTTATA
78024 AAACAAGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 8 0.28
13 21 0.72
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTTATATTTA
Found at i:78653 original size:33 final size:31
Alignment explanation
Indices: 78610--78674 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
78600 TCTCTTATTG
*
78610 AAAATAAATTAGGCCTTATTAACAAATTTAAAA
1 AAAATAAATTAAG-CTTATTAA-AAATTTAAAA
* * *
78643 AAAATCAATTAAGCTTTTTTAAAATTTAAAA
1 AAAATAAATTAAGCTTATTAAAAATTTAAAA
78674 A
1 A
78675 TTATTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 11 0.39
32 6 0.21
33 11 0.39
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.34
Consensus pattern (31 bp):
AAAATAAATTAAGCTTATTAAAAATTTAAAA
Found at i:80746 original size:171 final size:170
Alignment explanation
Indices: 80456--80785 Score: 527
Period size: 171 Copynumber: 1.9 Consensus size: 170
80446 TTCCTTTGCT
* * *
80456 ATGGGAGATACAAACATTTGACCTGAGGATGTAGGATCTAGAGATGTAGGAGAAAGGGAGCTGCT
1 ATGGGAGATACAAACATTTGACCTGAGGATG-AGGATCTAGAGAAGCAGGAGAAAAGGAGCTGCT
* * *
80521 ACAATTCCGATCCTGTAACTGATCCATCTCACCATGTGAAGGTGGCACAGGATCATGGGATTGAG
65 ACAATTACGATCCTCTAACTGATCCATCTCACCATGTGAAGGTGGCACAGGATCATGGAATTGAG
*
80586 TTTTGGGTAATTCTTTGGAGCAGCAAATACAAACTTTTTCC
130 TTTTGGGTAATTCTTTGGAGAAGCAAATACAAACTTTTTCC
*
80627 ATGGGAGATACAAACTTTTGACCTGAGGATG-GGTTATCTAGAGAAGCAGGAGAAAAGGAGCTGC
1 ATGGGAGATACAAACATTTGACCTGAGGATGAGG--ATCTAGAGAAGCAGGAGAAAAGGAGCTGC
* * *
80691 TACAATTACGTTCCTCTAACTGATCCATCTCATCATGTGAAGGTGGCAGAGGATCATGGAATTGA
64 TACAATTACGATCCTCTAACTGATCCATCTCACCATGTGAAGGTGGCACAGGATCATGGAATTGA
80756 GTTTTGGGTAATTCTTTGGAGAAGCAAATA
129 GTTTTGGGTAATTCTTTGGAGAAGCAAATA
80786 TGTTCCCCCT
Statistics
Matches: 146, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
169 2 0.01
171 144 0.99
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (170 bp):
ATGGGAGATACAAACATTTGACCTGAGGATGAGGATCTAGAGAAGCAGGAGAAAAGGAGCTGCTA
CAATTACGATCCTCTAACTGATCCATCTCACCATGTGAAGGTGGCACAGGATCATGGAATTGAGT
TTTGGGTAATTCTTTGGAGAAGCAAATACAAACTTTTTCC
Found at i:86002 original size:32 final size:31
Alignment explanation
Indices: 85950--86011 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
85940 TGAAATTCAA
85950 AAATTGATATAAACTTTAAACT-TCAAATTTG
1 AAATTGATATAAACTTTAAACTCT-AAATTTG
*
85981 AAATTCGATTTAAA-TTCTAAACTCTAAATTT
1 AAATT-GATATAAACTT-TAAACTCTAAATTT
86012 TTAGACTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 7 0.26
32 19 0.70
33 1 0.04
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (31 bp):
AAATTGATATAAACTTTAAACTCTAAATTTG
Found at i:87715 original size:17 final size:17
Alignment explanation
Indices: 87693--87740 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
87683 TAAGATTGAG
87693 TTAAGAAAATT-ATTTAA
1 TTAAG-AAATTAATTTAA
*
87710 TTAAGAAATTAATTTAG
1 TTAAGAAATTAATTTAA
**
87727 TTAATTAATTAATT
1 TTAAGAAATTAATT
87741 ATATTTTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
TTAAGAAATTAATTTAA
Found at i:87740 original size:21 final size:22
Alignment explanation
Indices: 87706--87746 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
87696 AGAAAATTAT
87706 TTAATTAAGAAATTA-ATTTAG
1 TTAATTAAGAAATTATATTTAG
**
87727 TTAATTAATTAATTATATTT
1 TTAATTAAGAAATTATATTT
87747 TGGATAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TTAATTAAGAAATTATATTTAG
Found at i:87781 original size:16 final size:18
Alignment explanation
Indices: 87760--87798 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
87750 ATAAGAGAAA
87760 ATAAAT-AT-AGGGTTGG
1 ATAAATCATAAGGGTTGG
*
87776 ATAAATCATAAGTGTTGG
1 ATAAATCATAAGGGTTGG
87794 ATAAA
1 ATAAA
87799 AACCAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 12 0.60
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.31
Consensus pattern (18 bp):
ATAAATCATAAGGGTTGG
Found at i:89232 original size:21 final size:21
Alignment explanation
Indices: 89200--89248 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
89190 CAGTAACAGT
* *
89200 CTTCTA-TCGATACTAGTGATA
1 CTTCTACT-GATACAAGTGACA
*
89221 GTTCTACTGATACAAGTGACA
1 CTTCTACTGATACAAGTGACA
89242 CTTCTAC
1 CTTCTAC
89249 CGAAATAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (21 bp):
CTTCTACTGATACAAGTGACA
Found at i:98290 original size:12 final size:12
Alignment explanation
Indices: 98273--98297 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
98263 TGTAATTCAC
98273 AAAAAAAAAACA
1 AAAAAAAAAACA
98285 AAAAAAAAAACA
1 AAAAAAAAAACA
98297 A
1 A
98298 CAACAACAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:103824 original size:12 final size:12
Alignment explanation
Indices: 103807--103832 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
103797 TGCAATCAAC
103807 ATAGAGGTGTTT
1 ATAGAGGTGTTT
103819 ATAGAGGTGTTT
1 ATAGAGGTGTTT
103831 AT
1 AT
103833 GGATTAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (12 bp):
ATAGAGGTGTTT
Found at i:105762 original size:59 final size:56
Alignment explanation
Indices: 105692--105978 Score: 243
Period size: 59 Copynumber: 4.9 Consensus size: 56
105682 TTTTGGACAC
* * * *
105692 TCGAGGGCAAAACGGCAATTTTCAAACACTCGGGGGCAAAATGGTAATTTTTGGAAGAT
1 TCGAGGTCAAAATGG-AATTTT-AGACA-TCGGGGGTAAAATGGTAATTTTTGGAAGAT
* * *
105751 TCGAGGTCAAAAATGGAATTTTTAGACATCCAGGGGTAAAATGGTAATTTTTGAAATAT
1 TCGAGGTC-AAAATGGAA-TTTTAGACAT-CGGGGGTAAAATGGTAATTTTTGGAAGAT
* * *
105810 TCGGGGTTAAAATGGAATTGTTAGACATTCGGGGGTAAAATGCTAATTTTTGGAA-AGT
1 TCGAGGTCAAAATGGAATT-TTAGACA-TCGGGGGTAAAATGGTAATTTTTGGAAGA-T
** *** **
105868 TTTAGGGTCAAAATGGAATTTTTAGACATTTAAGGGTAAAATGGTAATTTTTAAAAGAT
1 TCGA-GGTCAAAATGGAA-TTTTAGACA-TCGGGGGTAAAATGGTAATTTTTGGAAGAT
* * * **
105927 TCTAGGTTAAAATGAAATTTTTAGACATCCGAAGGTAAAATGGTAATTTTTG
1 TCGAGGTCAAAATGGAA-TTTTAGACAT-CGGGGGTAAAATGGTAATTTTTG
105979 AAAAGTTTAG
Statistics
Matches: 189, Mismatches: 29, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
57 4 0.02
58 82 0.43
59 90 0.48
60 13 0.07
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (56 bp):
TCGAGGTCAAAATGGAATTTTAGACATCGGGGGTAAAATGGTAATTTTTGGAAGAT
Found at i:105801 original size:28 final size:27
Alignment explanation
Indices: 105724--105977 Score: 139
Period size: 29 Copynumber: 8.7 Consensus size: 27
105714 CAAACACTCG
* * *
105724 GGGGCAAAATGGTAATTTTTGGAAGATTC
1 GGGGTAAAATGG-AATTTTTAG-ACATTC
* *
105753 GAGGTCAAAAATGGAATTTTTAGACATCC
1 GGGGT--AAAATGGAATTTTTAGACATTC
* *
105782 AGGGGTAAAATGGTAATTTTTGAAATATTC
1 -GGGGTAAAATGG-AATTTTT-AGACATTC
*
105812 GGGGTTAAAATGGAATTGTTAGACATTC
1 GGGG-TAAAATGGAATTTTTAGACATTC
* * * *
105840 GGGGGTAAAATGCTAATTTTTGGAAAGTTTT
1 -GGGGTAAAATG-GAATTTTTAGACA--TTC
* *
105871 AGGGTCAAAATGGAATTTTTAGACATTTA
1 GGGGT-AAAATGGAATTTTTAGACA-TTC
* * *
105900 AGGGTAAAATGGTAATTTTTAAAAGATTC
1 GGGGTAAAATGG-AATTTTT-AGACATTC
* * * *
105929 TAGGTTAAAATGAAATTTTTAGACATCC
1 -GGGGTAAAATGGAATTTTTAGACATTC
*
105957 GAAGGTAAAATGGTAATTTTT
1 G-GGGTAAAATGG-AATTTTT
105978 GAAAAGTTTA
Statistics
Matches: 175, Mismatches: 34, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
28 40 0.23
29 68 0.39
30 52 0.30
31 15 0.09
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (27 bp):
GGGGTAAAATGGAATTTTTAGACATTC
Found at i:105886 original size:117 final size:117
Alignment explanation
Indices: 105721--106003 Score: 381
Period size: 117 Copynumber: 2.4 Consensus size: 117
105711 TTTCAAACAC
* * * *
105721 TCGGGGGCAAAATGGTAATTTTTGG-AAGATTCGAGGTCAAAAATGGAATTTTTAGACATCCAGG
1 TCGGGGGTAAAATGGTAATTTTTGGAAAGTTTAG-GGTCAAAAATGGAATTTTTAGACATCCAAG
* * * *
105785 GGTAAAATGGTAATTTTTGAAATATTCGGGGTTAAAATGGAATTGTTAGACAT
65 GGTAAAATGGTAATTTTTAAAAGATTCGAGGTTAAAATGAAATTGTTAGACAT
* **
105838 TCGGGGGTAAAATGCTAATTTTTGGAAAGTTTTAGGGTC-AAAATGGAATTTTTAGACATTTAAG
1 TCGGGGGTAAAATGGTAATTTTTGGAAAG-TTTAGGGTCAAAAATGGAATTTTTAGACATCCAAG
* *
105902 GGTAAAATGGTAATTTTTAAAAGATTCTAGGTTAAAATGAAATTTTTAGACAT
65 GGTAAAATGGTAATTTTTAAAAGATTCGAGGTTAAAATGAAATTGTTAGACAT
* ** *
105955 CCGAAGGTAAAATGGTAATTTTTGAAAAGTTTAGGGTCAAAAATGGAAT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTCAAAAATGGAAT
106004 CTTGGAAAGT
Statistics
Matches: 145, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
116 9 0.06
117 126 0.87
118 7 0.05
119 3 0.02
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (117 bp):
TCGGGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTCAAAAATGGAATTTTTAGACATCCAAGG
GTAAAATGGTAATTTTTAAAAGATTCGAGGTTAAAATGAAATTGTTAGACAT
Found at i:106015 original size:29 final size:29
Alignment explanation
Indices: 105963--106075 Score: 122
Period size: 29 Copynumber: 3.8 Consensus size: 29
105953 ATCCGAAGGT
*
105963 AAAATGGTAATTTTTGAAAAGTTTAGGGTCA
1 AAAATGG-AA-TTTTGGAAAGTTTAGGGTCA
*
105994 AAAATGGAATCTTGGAAAGTTTAGGGGT--
1 AAAATGGAATTTTGGAAAGTTTA-GGGTCA
* * *
106022 AAAATGCACTTTTTAGAAAGTTTAGGGTCA
1 AAAATGGA-ATTTTGGAAAGTTTAGGGTCA
*
106052 AAAATGGAATTTTGGTAAGTTTAG
1 AAAATGGAATTTTGGAAAGTTTAG
106076 TGGAAAAATA
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
28 11 0.16
29 37 0.54
30 13 0.19
31 7 0.10
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTGGAAAGTTTAGGGTCA
Found at i:106025 original size:59 final size:59
Alignment explanation
Indices: 105724--106064 Score: 317
Period size: 58 Copynumber: 5.8 Consensus size: 59
105714 CAAACACTCG
* * * * *
105724 GGGGCAAAATGGTAATTTTTG-GAAGATTCGAGGTCAAAAATGGAATTTTTAGACATCCA
1 GGGGTAAAATGGTAATTTTTGAAAAGTTTAG-GGTCAAAAATGGAATTTTTAGACATTCA
** * * *
105783 GGGGTAAAATGGTAATTTTTGAAATA-TTCGGGGT-TAAAATGGAATTGTTAGACATTCG
1 GGGGTAAAATGGTAATTTTTGAAA-AGTTTAGGGTCAAAAATGGAATTTTTAGACATTCA
* * *
105841 GGGGTAAAATGCTAATTTTTGGAAAGTTTTAGGGTC-AAAATGGAATTTTTAGACATTTA
1 GGGGTAAAATGGTAATTTTTGAAAAG-TTTAGGGTCAAAAATGGAATTTTTAGACATTCA
* * * *
105900 AGGGTAAAATGGTAATTTTT-AAAAGATTCTA-GGT-TAAAATGAAATTTTTAGACA-TCC
1 GGGGTAAAATGGTAATTTTTGAAAAG-TT-TAGGGTCAAAAATGGAATTTTTAGACATTCA
* * * * *
105957 GAAGGTAAAATGGTAATTTTTGAAAAGTTTAGGGTCAAAAATGGAA-TCTTGGAAAGTTTA
1 G-GGGTAAAATGGTAATTTTTGAAAAGTTTAGGGTCAAAAATGGAATTTTTAGACA-TTCA
* *
106017 GGGGTAAAAT-GCACTTTTT-AGAAAGTTTAGGGTCAAAAATGGAATTTT
1 GGGGTAAAATGGTAATTTTTGA-AAAGTTTAGGGTCAAAAATGGAATTTT
106065 GGTAAGTTTA
Statistics
Matches: 231, Mismatches: 36, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
57 5 0.02
58 128 0.55
59 92 0.40
60 5 0.02
61 1 0.00
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGAAAAGTTTAGGGTCAAAAATGGAATTTTTAGACATTCA
Found at i:106056 original size:117 final size:117
Alignment explanation
Indices: 105755--106064 Score: 306
Period size: 117 Copynumber: 2.6 Consensus size: 117
105745 GAAGATTCGA
* * ** * * * * ** *
105755 GGTCAAAAATGGAATTTTTAGACATCCAGGGGTAAAATGGTAATTTTTGAAATATTCGGGGTTAA
1 GGTC-AAAATGGAATTCTTAGAAATTTAAGGGTAAAATGGCAATTTTTAAAAGATTCTAGGTAAA
* * ** *
105820 AATGGAATTGTTAGACATTCGGGGGTAAAATGCTAATTTTTGGAAAGTTTTAG
65 AATGGAATTTTTAGACATCCGAAGGTAAAATGCTAATTTTTGAAAAGTTTTAG
* * * *
105873 GGTCAAAATGGAATTTTTAGACATTTAAGGGTAAAATGGTAATTTTTAAAAGATTCTAGGTTAAA
1 GGTCAAAATGGAATTCTTAGAAATTTAAGGGTAAAATGGCAATTTTTAAAAGATTCTAGGTAAAA
* *
105938 ATGAAATTTTTAGACATCCGAAGGTAAAATGGTAATTTTTGAAAAG-TTTAG
66 ATGGAATTTTTAGACATCCGAAGGTAAAATGCTAATTTTTGAAAAGTTTTAG
* * *
105989 GGTCAAAAATGGAA-TCTTGGAAAGTTTAGGGGTAAAAT-GCACTTTTTAGAAAG-TT-TAGGGT
1 GGTC-AAAATGGAATTCTTAGAAA-TTTAAGGGTAAAATGGCAATTTTTA-AAAGATTCTA-GGT
106050 CAAAAATGGAATTTT
62 -AAAAATGGAATTTT
106065 GGTAAGTTTA
Statistics
Matches: 165, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
115 2 0.01
116 28 0.17
117 131 0.79
118 4 0.02
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (117 bp):
GGTCAAAATGGAATTCTTAGAAATTTAAGGGTAAAATGGCAATTTTTAAAAGATTCTAGGTAAAA
ATGGAATTTTTAGACATCCGAAGGTAAAATGCTAATTTTTGAAAAGTTTTAG
Found at i:106102 original size:58 final size:58
Alignment explanation
Indices: 105971--106093 Score: 158
Period size: 58 Copynumber: 2.1 Consensus size: 58
105961 GTAAAATGGT
* *
105971 AATTTTT-GAAAAGTTTAGGGTCAAAAATGGAATCTTGGAAAGTTTAGGGGTAAAATGC
1 AATTTTTAG-AAAGTTTAGGGTCAAAAATGGAATCTTGGAAAGTTTAGGGGAAAAATGA
* * * * *
106029 ACTTTTTAGAAAGTTTAGGGTCAAAAATGGAATTTTGGTAAGTTTAGTGGAAAAATATA
1 AATTTTTAGAAAGTTTAGGGTCAAAAATGGAATCTTGGAAAGTTTAGGGGAAAAAT-GA
106088 AATTTT
1 AATTTT
106094 GTGAAGTTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 49 0.89
59 6 0.11
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (58 bp):
AATTTTTAGAAAGTTTAGGGTCAAAAATGGAATCTTGGAAAGTTTAGGGGAAAAATGA
Found at i:108005 original size:17 final size:17
Alignment explanation
Indices: 107943--107992 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
107933 AACTTTTGAT
*
107943 TAAATTTTAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
107960 TAAATTTAAACTCAAAA
1 TAAATTTAAATTTAAAA
*
107977 TAAGTTTAAATTTAAA
1 TAAATTTAAATTTAAA
107993 CTTAAAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:108010 original size:23 final size:23
Alignment explanation
Indices: 107961--108015 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
107951 AATTTAAAAT
* *
107961 AAATTTAAACTCAAAATAAGTTT
1 AAATTTAAACTCAAAATAAATTA
*
107984 AAATTTAAACTTAAAATAAATTA
1 AAATTTAAACTCAAAATAAATTA
*
108007 AAATCTAAA
1 AAATTTAAA
108016 AAATTCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATTTAAACTCAAAATAAATTA
Found at i:108978 original size:10 final size:11
Alignment explanation
Indices: 108948--108977 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
108938 GAGCAAAAGG
108948 AGCGAAAAACA
1 AGCGAAAAACA
108959 AGCGAAAAACA
1 AGCGAAAAACA
108970 AGCGAAAA
1 AGCGAAAA
108978 CCGGACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.17, G:0.20, T:0.00
Consensus pattern (11 bp):
AGCGAAAAACA
Found at i:109268 original size:23 final size:24
Alignment explanation
Indices: 109242--109287 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
109232 CCAATTAGAG
109242 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCT-TTTAGAATTTAATTCT
109265 AATTATCCTTTTAGAATTTAATT
1 AATTAT-CTTTTAGAATTTAATT
109288 TAGATTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (24 bp):
AATTATCTTTTAGAATTTAATTCT
Found at i:117736 original size:31 final size:31
Alignment explanation
Indices: 117701--117761 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
117691 TGATCATTTT
**
117701 TAGTCCTTGTAATTTTTGAATTTTGAAATTA
1 TAGTCCTTGTAATTTCCGAATTTTGAAATTA
*
117732 TAGTCCTTGTACTTTCCGAATTTTGAAATT
1 TAGTCCTTGTAATTTCCGAATTTTGAAATT
117762 TAAAATTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (31 bp):
TAGTCCTTGTAATTTCCGAATTTTGAAATTA
Found at i:125115 original size:21 final size:19
Alignment explanation
Indices: 125083--125123 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
125073 TTTTTCAAAT
*
125083 AATTAAGTTTATTTTCTTTA
1 AATTAAGGTTATTTT-TTTA
125103 AATTAAGAGTTATTTTTTTA
1 AATTAAG-GTTATTTTTTTA
125123 A
1 A
125124 TTTCATGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.56
Consensus pattern (19 bp):
AATTAAGGTTATTTTTTTA
Found at i:130221 original size:2 final size:2
Alignment explanation
Indices: 130214--130246 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
130204 TCCTAAAATA
130214 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.